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Sample GSM7441184 Query DataSets for GSM7441184
Status Public on Jun 07, 2023
Title Adult intestinal esg+ cells, control batch1, rep1
Sample type SRA
Source name Adult midgut
Organism Drosophila melanogaster
Characteristics tissue: Adult midgut
cell type: esg-positive cells
genotype: esg-Gal4, UAS-GFP, tub-Gal80[ts]
treatment: temperature switch 18>29C
Treatment protocol Switched to 29ºC in normal food for 2 days prior to dissection.
Growth protocol Flies maintained at 18ºC in normal food until adulthood.
Extracted molecule total RNA
Extraction protocol We dissected 100 midguts/genotype in triplicate and for each sample 20,000–40,000 cells were sorted into RNAse-free 1× PBS with 5 mM EDTA. RNA was isolated using the Arcturus PicoPure™ RNA Isolation Kit.
The entire amount of isolated RNA was used as input for RNA-amplification using the Arcturus™ RiboAmp™ HS PLUS Kit. Two hundred nanograms of amplified aRNA was used as input for RNA-Seq library preparation using the TruSeq Stranded mRNA Library Prep Kit (Illumina)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description 1x50bp
Data processing map with `--readFilesCommand zcat --outMultimapperOrder Random --outSAMmultNmax 1 --runMode alignReads --outSAMtype BAM Unsorted --quantMode GeneCounts`
index with `bamtools index -in aligned.bam -out indexed.bam`
sort with `bamtools sort -out sorted.bam -in indexed.bam`
count reads per gene with `featureCounts -T 8 -p -C -F GTF -t exon -g gene_id ...`
Assembly: FB2019_03 Dmel Release 6.28
Supplementary files format and content: .featurecounts files contain the mapping of reads to each gene in plain text (tab-delimited)
Supplementary files format and content: .summary files contain summary statistics of the mapping in plain text
Submission date Jun 02, 2023
Last update date Jun 07, 2023
Contact name Joaquin de Navascues Melero
Organization name University of Essex
Department School of Life Sciences
Street address Wivenhoe Park
City Colchester
State/province Essex
ZIP/Postal code CO4 3SQ
Country United Kingdom
Platform ID GPL17275
Series (1)
GSE234019 Homo- and heterodimerization of bHLH transcription factors balance stemness and bipotential differentiation in the Drosophila adult intestine
BioSample SAMN35574018
SRA SRX20581238

Supplementary file Size Download File type/resource
GSM7441184_C3N4AACXX_1.featurecount.summary.txt.gz 292 b (ftp)(http) TXT
GSM7441184_C3N4AACXX_1.featurecount.txt.gz 823.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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